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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs12722495

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr10:6055320 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.070066 (8798/125568, TOPMED)
C=0.06461 (2026/31358, GnomAD)
C=0.0872 (483/5538, ALFA Project) (+ 10 more)
C=0.0347 (174/5008, 1000G)
C=0.0690 (309/4480, Estonian)
C=0.1131 (436/3854, ALSPAC)
C=0.1130 (419/3708, TWINSUK)
C=0.102 (102/998, GoNL)
C=0.070 (42/600, NorthernSweden)
C=0.060 (13/216, Qatari)
T=0.44 (14/32, SGDP_PRJ)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IL2RA : Intron Variant
Publications
14 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 10 NC_000010.11:g.6055320T>C
GRCh37.p13 chr 10 NC_000010.10:g.6097283T>C
IL2RA RefSeqGene (LRG_73) NG_007403.1:g.11990A>G
Gene: IL2RA, interleukin 2 receptor subunit alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IL2RA transcript variant 1 NM_000417.3:c.64+6768A>G N/A Intron Variant
IL2RA transcript variant 2 NM_001308242.2:c.64+6768A…

NM_001308242.2:c.64+6768A>G

N/A Intron Variant
IL2RA transcript variant 3 NM_001308243.2:c.64+6768A…

NM_001308243.2:c.64+6768A>G

N/A Intron Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 5538 T=0.9128 C=0.0872
European Sub 4240 T=0.8929 C=0.1071
African Sub 1194 T=0.9807 C=0.0193
African Others Sub 36 T=1.00 C=0.00
African American Sub 1158 T=0.9801 C=0.0199
Asian Sub 4 T=1.0 C=0.0
East Asian Sub 2 T=1.0 C=0.0
Other Asian Sub 2 T=1.0 C=0.0
Latin American 1 Sub 0 T=0 C=0
Latin American 2 Sub 0 T=0 C=0
South Asian Sub 4 T=0.8 C=0.2
Other Sub 96 T=0.95 C=0.05


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.929934 C=0.070066
gnomAD - Genomes Global Study-wide 31358 T=0.93539 C=0.06461
gnomAD - Genomes European Sub 18882 T=0.91081 C=0.08919
gnomAD - Genomes African Sub 8700 T=0.9784 C=0.0216
gnomAD - Genomes East Asian Sub 1558 T=0.9974 C=0.0026
gnomAD - Genomes Other Sub 1082 T=0.9316 C=0.0684
gnomAD - Genomes American Sub 846 T=0.942 C=0.058
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.907 C=0.093
ALFA Total Global 5538 T=0.9128 C=0.0872
ALFA European Sub 4240 T=0.8929 C=0.1071
ALFA African Sub 1194 T=0.9807 C=0.0193
ALFA Other Sub 96 T=0.95 C=0.05
ALFA South Asian Sub 4 T=0.8 C=0.2
ALFA Asian Sub 4 T=1.0 C=0.0
ALFA Latin American 1 Sub 0 T=0 C=0
ALFA Latin American 2 Sub 0 T=0 C=0
1000Genomes Global Study-wide 5008 T=0.9653 C=0.0347
1000Genomes African Sub 1322 T=0.9932 C=0.0068
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9225 C=0.0775
1000Genomes South Asian Sub 978 T=0.940 C=0.060
1000Genomes American Sub 694 T=0.960 C=0.040
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9310 C=0.0690
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8869 C=0.1131
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8870 C=0.1130
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.898 C=0.102
Northern Sweden ACPOP Study-wide 600 T=0.930 C=0.070
Qatari Global Study-wide 216 T=0.940 C=0.060
SGDP_PRJ Global Study-wide 32 T=0.44 C=0.56
Siberian Global Study-wide 4 T=0.5 C=0.5
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= C
GRCh38.p12 chr 10 NC_000010.11:g.6055320= NC_000010.11:g.6055320T>C
GRCh37.p13 chr 10 NC_000010.10:g.6097283= NC_000010.10:g.6097283T>C
IL2RA RefSeqGene (LRG_73) NG_007403.1:g.11990= NG_007403.1:g.11990A>G
IL2RA transcript variant 1 NM_000417.2:c.64+6768= NM_000417.2:c.64+6768A>G
IL2RA transcript variant 1 NM_000417.3:c.64+6768= NM_000417.3:c.64+6768A>G
IL2RA transcript variant 2 NM_001308242.2:c.64+6768= NM_001308242.2:c.64+6768A>G
IL2RA transcript variant 3 NM_001308243.2:c.64+6768= NM_001308243.2:c.64+6768A>G
IL2RA transcript variant X1 XM_005252446.1:c.64+6768= XM_005252446.1:c.64+6768A>G
IL2RA transcript variant X2 XM_005252447.1:c.64+6768= XM_005252447.1:c.64+6768A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

38 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss20422831 Apr 05, 2004 (121)
2 JDRF_WT_DIL ss52580003 Oct 14, 2006 (127)
3 BCMHGSC_JDW ss88080047 Mar 23, 2008 (129)
4 1000GENOMES ss109195663 Jan 23, 2009 (130)
5 ILLUMINA ss172232943 Jul 04, 2010 (132)
6 1000GENOMES ss235037190 Jul 15, 2010 (132)
7 EVA-GONL ss987155196 Aug 21, 2014 (142)
8 JMKIDD_LAB ss1076730097 Aug 21, 2014 (142)
9 1000GENOMES ss1336122689 Aug 21, 2014 (142)
10 DDI ss1426208083 Apr 01, 2015 (144)
11 EVA_DECODE ss1596802917 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1623907802 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1666901835 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1930475941 Feb 12, 2016 (147)
15 JJLAB ss2025960854 Sep 14, 2016 (149)
16 ILLUMINA ss2094857964 Dec 20, 2016 (150)
17 ILLUMINA ss2095004862 Dec 20, 2016 (150)
18 USC_VALOUEV ss2154202869 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2172343752 Dec 20, 2016 (150)
20 TOPMED ss2335053113 Dec 20, 2016 (150)
21 GNOMAD ss2885085116 Nov 08, 2017 (151)
22 AFFY ss2985550135 Nov 08, 2017 (151)
23 SWEGEN ss3005872104 Nov 08, 2017 (151)
24 ILLUMINA ss3021210564 Nov 08, 2017 (151)
25 BIOINF_KMB_FNS_UNIBA ss3026764021 Nov 08, 2017 (151)
26 TOPMED ss3110618921 Nov 08, 2017 (151)
27 CSHL ss3348940782 Nov 08, 2017 (151)
28 ILLUMINA ss3637831673 Oct 12, 2018 (152)
29 ILLUMINA ss3651558061 Oct 12, 2018 (152)
30 ILLUMINA ss3651558062 Oct 12, 2018 (152)
31 EGCUT_WGS ss3673399440 Jul 13, 2019 (153)
32 EVA_DECODE ss3689202199 Jul 13, 2019 (153)
33 ILLUMINA ss3725132106 Jul 13, 2019 (153)
34 ACPOP ss3737024792 Jul 13, 2019 (153)
35 EVA ss3747696958 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3813060036 Jul 13, 2019 (153)
37 EVA ss3831945797 Apr 26, 2020 (154)
38 SGDP_PRJ ss3873449084 Apr 26, 2020 (154)
39 1000Genomes NC_000010.10 - 6097283 Oct 12, 2018 (152)
40 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 6097283 Oct 12, 2018 (152)
41 Genetic variation in the Estonian population NC_000010.10 - 6097283 Oct 12, 2018 (152)
42 gnomAD - Genomes NC_000010.10 - 6097283 Jul 13, 2019 (153)
43 Genome of the Netherlands Release 5 NC_000010.10 - 6097283 Apr 26, 2020 (154)
44 Northern Sweden NC_000010.10 - 6097283 Jul 13, 2019 (153)
45 Qatari NC_000010.10 - 6097283 Apr 26, 2020 (154)
46 SGDP_PRJ NC_000010.10 - 6097283 Apr 26, 2020 (154)
47 Siberian NC_000010.10 - 6097283 Apr 26, 2020 (154)
48 TopMed NC_000010.11 - 6055320 Oct 12, 2018 (152)
49 UK 10K study - Twins NC_000010.10 - 6097283 Oct 12, 2018 (152)
50 dbGaP Population Frequency Project NC_000010.11 - 6055320 Apr 26, 2020 (154)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss88080047, ss109195663, ss1596802917, ss2094857964 NC_000010.9:6137288:T:C NC_000010.11:6055319:T:C (self)
48463703, 26927690, 19137688, 132539162, 12010254, 10309657, 12517871, 25466064, 6719223, 26927690, ss235037190, ss987155196, ss1076730097, ss1336122689, ss1426208083, ss1623907802, ss1666901835, ss1930475941, ss2025960854, ss2095004862, ss2154202869, ss2335053113, ss2885085116, ss2985550135, ss3005872104, ss3021210564, ss3348940782, ss3637831673, ss3651558061, ss3651558062, ss3673399440, ss3737024792, ss3747696958, ss3831945797, ss3873449084 NC_000010.10:6097282:T:C NC_000010.11:6055319:T:C (self)
35648140, 16170251, ss2172343752, ss3026764021, ss3110618921, ss3689202199, ss3725132106, ss3813060036 NC_000010.11:6055319:T:C NC_000010.11:6055319:T:C (self)
ss20422831, ss52580003, ss172232943 NT_008705.16:6037282:T:C NC_000010.11:6055319:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

14 citations for rs12722495
PMID Title Author Year Journal
19073967 Shared and distinct genetic variants in type 1 diabetes and celiac disease. Smyth DJ et al. 2008 The New England journal of medicine
19701192 Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource. Dendrou CA et al. 2009 Nature genetics
19956106 Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families. Howson JM et al. 2009 Genes and immunity
20805105 Synthetic associations in the context of genome-wide association scan signals. Orozco G et al. 2010 Human molecular genetics
21179116 An autoimmune-associated variant in PTPN2 reveals an impairment of IL-2R signaling in CD4(+) T cells. Long SA et al. 2011 Genes and immunity
21266329 Tests for genetic interactions in type 1 diabetes: linkage and stratification analyses of 4,422 affected sib-pairs. Morahan G et al. 2011 Diabetes
21829393 Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. Plagnol V et al. 2011 PLoS genetics
21873553 Genetic analysis of adult-onset autoimmune diabetes. Howson JM et al. 2011 Diabetes
22770979 Presence of multiple independent effects in risk loci of common complex human diseases. Ke X et al. 2012 American journal of human genetics
23804261 From markers to molecular mechanisms: type 1 diabetes in the post-GWAS era. Baxter AG et al. 2012 The review of diabetic studies
26106387 Pathogenesis of Systemic Sclerosis. Pattanaik D et al. 2015 Frontiers in immunology
26133380 Associations of Independent IL2RA Gene Variants with Intermediate Uveitis. Lindner E et al. 2015 PloS one
28870212 Chromosome contacts in activated T cells identify autoimmune disease candidate genes. Burren OS et al. 2017 Genome biology
31808541 Type 1 diabetes linked PTPN22 gene polymorphism is associated with the frequency of circulating regulatory T cells. Valta M et al. 2020 European journal of immunology
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post536+f5d31d6